{"id":431,"date":"2024-04-25T20:16:34","date_gmt":"2024-04-25T20:16:34","guid":{"rendered":"https:\/\/winterdev.cc\/nwgc-dev\/?page_id=431"},"modified":"2024-09-10T15:29:46","modified_gmt":"2024-09-10T15:29:46","slug":"data-delivery","status":"publish","type":"page","link":"https:\/\/nwgc.gs.washington.edu\/wordpress\/services\/structural-genomics\/short-read\/wes\/data-delivery\/","title":{"rendered":"Data Delivery"},"content":{"rendered":"<p>Data delivery varies depending on the specifics of the project. Factors that influence the type of data returned include species and library construction method.<\/p>\n<h3 class=\"wp-block-heading\">For Human WGS and Exome Projects:<\/h3>\n<ul class=\"wp-block-list\">\n<li>bam file (*.bam) &#8211; is a binary SAM file that contains the sequence alignment data for a single sample created using BWA<\/li>\n<li>bam index file (*.bam.bai) &#8211; are the index files for the corresponding bam files<\/li>\n<li>Multi-sample vcf file (.vcf) &#8211; contains all samples in a project called at every site that is variant in at least one of the samples as generally recommended by GATK best practices. For more information on VCF format check <a href=\"http:\/\/www.1000genomes.org\/wiki\/Analysis\/Variant%20Call%20Format\/vcf-variant-call-format-version-41\">here.<\/a><\/li>\n<li>Sample ID Lookup table (.xls) &#8211; is a cross-reference between the UW-CMG LIMS IDs generated at the sequencing center and the investigator sample IDs. It also lists the family information for the project.<\/li>\n<li>Genotype data &#8211; Not all projects will have high-density genotyping data generated. If the project was genotyped, the investigator will receive a PLINK-formatted file containing the genotypes. For more information on PLINK, go <a href=\"https:\/\/zzz.bwh.harvard.edu\/plink\/tutorial.shtml\">here.<\/a><\/li>\n<\/ul>\n<p>*FASTQs can be released for any project type<\/p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Data delivery varies depending on the specifics of the project. Factors that influence the type of data returned include species and library construction method. For Human WGS and Exome Projects: *FASTQs can be released for any project type<\/p>\n<div><a class=\"more-link\" href=\"https:\/\/nwgc.gs.washington.edu\/wordpress\/services\/structural-genomics\/short-read\/wes\/data-delivery\/\">Continue reading <span class=\"screen-reader-text\">Data Delivery<\/span><\/a><\/div>\n","protected":false},"author":2,"featured_media":0,"parent":328,"menu_order":6,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-431","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/pages\/431","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/comments?post=431"}],"version-history":[{"count":1,"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/pages\/431\/revisions"}],"predecessor-version":[{"id":2272,"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/pages\/431\/revisions\/2272"}],"up":[{"embeddable":true,"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/pages\/328"}],"wp:attachment":[{"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/media?parent=431"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}